Wander through the streets of Damascus this week, and you will see signs everywhere of the conflict in Lebanon. The bearded, black-turbaned Hassan Nasrallah stares out from every shop window, even in the Christian quarter. Here electric-blue neon crosses wink from the domes of the churches, and processions of crucifix-carrying boy scouts squeeze past gaggles of Christian girls heading out on the town, all low-cut jeans and tight-fitting T-shirts. The video shops are full of DVDs showing "highlights" from the war - exploding Israeli tanks and jubilant Hizbullah fighters - which sell even better than the ubiquitous pirated versions of the latest Hollywood releases, The Devil Wears Prada and The Da Vinci Code: evidence that in the contemporary Middle East you don't have to hate western culture, or even be a Muslim, to relish the bloody nose given to ill-judged Israeli and American attempts at imposing their hegemony in the region by force of invasion and cluster bombs.

Evidence of the conflict in Iraq, Syria's neighbour to the north-east, is at first harder to spot than the ubiquitous images from Lebanon, but on closer examination it is no less pervasive. Lounging in every park and teahouse are unshaven, tired-looking Iraqi refugees, driven from their homes by sectarian mayhem. This summer, as Baghdad spiralled out of control, with more violent deaths in one fortnight than in Israel and Lebanon together in nearly a month of warfare, Syria responded by providing asylum (though not work permits) to all Iraqis who were forced to flee, as well as free education for their children.

Talk to the refugees in Damascus, however, and you soon find that one group predominates: the Iraqi Christians. Although they made up only about 3% of the population of prewar Iraq - 700,000 people - under Saddam they were a prosperous minority, symbolised by the high profile of Tariq Aziz, Saddam's Christian foreign minister. Highly educated and overwhelmingly middle class, the Christians were heavily concentrated in Mosul, Basra and especially Baghdad, which before the war had the largest Christian population of any Middle Eastern town or city.

Now at least half of these Christians - around 350,000 people - have fled Bush's new Iraq and its violence, mass abductions and economic meltdown. Wherever I went in Syria I kept running into them - bank managers and engineers, pharmacists and scientists, garage owners and businessmen - all living with their extended families in one-room flats on what remained of their savings, and assisted by the charity of the different churches.

"Before the war there was no separation between Christian and Muslim," I was told by Shamun Daawd, a former liquor-store owner who fled after he received Islamist death threats. "Under Saddam no one asked you your religion, and we used to attend each other's religious services and weddings. After the invasion we hoped democracy would come; but instead all that came was bombs, kidnapping and killing. Now at least 75% of my Christian friends have fled. There is no future for us in Iraq."

His friend Sabah Mansur Nesco told a similar tale when I met him at the Syrian Orthodox Patriarchate, where he had come to collect the rent money it provides for its more impoverished laity. He had lived in a wealthy mixed area of Baghdad, al-Doura, he said, until two of his nephews were kidnapped: for the first they had to arrange a $30,000 ransom; for the second $10,000. The boys were returned, having been tortured and beaten. Then some Christian neighbours were killed by jihadis. Five Baghdad churches were bombed, and stories began to circulate that Christian girls were getting raped at the university. The family decided enough was enough, and drove to Damascus.

The Christian community in Iraq is one of the oldest in the world, and has existed since the first century; according to tradition it was St Thomas and his cousin Addai who first brought Christianity to the Parthian capital of Seleucia-Ctesiphon soon after the resurrection. At the Council of Nicaea, where the words of the Christian creed were thrashed out in 325 AD, there were more bishops from Mesopotamia and India than there were from western Europe.

Later, the region became a refuge for groups considered heretical by the Orthodox Byzantine emperors - such as the Mandeans, the world's last surviving Gnostic sect, who follow what they believe to be the teachings of John the Baptist; and the Church of the East, or Nestorians, who played a key part in bringing Greek philosophy, science and medicine to the Islamic world. It was from the Nestorian school of Nisibis, via Córdoba, that many of Aristotle's and Plato's works reached the universities of medieval Europe. Yet in three years most members of this ancient church, and almost all the Mandeans, have been forced to flee the anarchy their western coreligionists have helped unleash.

This is part of a much wider problem across the Middle East. Almost everywhere the Christians are leaving, as ill-judged Anglo-American adventures, intended to suppress terrorism, actually have the reverse effect and steadily radicalise the entire region. Today in the Middle East the Arab Christians are a small minority of 12 million; in the last decade at least two million have left to make new lives for themselves in Europe, Australia and America. Only in Syria has this pattern been resisted.

Now there are worries that Syria, one of the last countries in the region without an Islamist movement, is also in Washington's cross hairs: Donald Rumsfeld, among others, has accused Syria of sponsoring the Islamic resistance in Iraq and in Lebanon.

Few would deny that Syria has much to reform. It is a one-party Ba'athist state, where political activists are suppressed and an extensive network of secret police fills the prisons with political prisoners. Violent opposition to the regime is met with overwhelming force, most dramatically in the case of the armed rising of the Muslim Brotherhood in Hama in 1982. The city was sealed off and at least 10,000 people were killed - a similar operation to that undertaken by the US in Falluja, except that Syria did not use banned chemical weapons.

Yet if Syria is a one-party police state, it is one that tends to leave its citizens alone as long as they keep out of politics. And if political freedoms have always been severely, and often brutally, restricted - as is also the case in most of the US's ally states in the region - Assad's regime does allow wide-ranging cultural and religious freedoms, which give Syria's minorities a security and stability far greater than their counterparts anywhere else in the region. This is particularly true of Syria's ancient Christian communities.

The Assads are Alawite, a Shia Muslim minority seen by orthodox Sunni Muslims as heretical, and disparagingly referred to as Nusayris, or Little Christians: indeed their liturgy seems to be partly Christian in origin. The Assads have stayed in power by forming in effect a coalition of religious minorities, through which they were able to counterbalance the weight of the Sunni majority. In Syria the major Christian feasts are national holidays; Christians are exempt from turning up to work on Sunday mornings; and churches and monasteries, like mosques, are given free electricity. This is unknown anywhere else in the Middle East.

It would be tragic if the British now assisted the US in destabilising not just Iraq and Lebanon, but also Syria. As Sabah Mansur Nesco put it: "Bush brought nothing but killing, violence and mass emigration - not just to Iraq but to Afghanistan and Palestine also. Now we just pray he leaves Syria alone. For us it is the last place of refuge."

· William Dalrymple is the author of From the Holy Mountain: A Journey in the Shadow of Byzantium. His new book, The Last Mughal, will be published by Bloomsbury next month